biobb-io 4.2.0__tar.gz → 5.0.0__tar.gz

{biobb_io-4.2.0 → biobb_io-5.0.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biobb_io
-Version: 4.2.0
+Version: 5.0.0
 Summary: Biobb_io is the Biobb module collection to fetch data to be consumed by the rest of the Biobb building blocks.
 Home-page: https://github.com/bioexcel/biobb_io
 Author: Biobb developers
@@ -8,24 +8,23 @@ Author-email: pau.andrio@bsc.es
 Project-URL: Documentation, http://biobb-io.readthedocs.io/en/latest/
 Project-URL: Bioexcel, https://bioexcel.eu/
 Keywords: Bioinformatics Workflows BioExcel Compatibility
-Classifier: Development Status :: 3 - Alpha
-Classifier: Programming Language :: Python :: 3.8
+Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: POSIX
-Requires-Python: >=3.8
+Classifier: Operating System :: Unix
+Requires-Python: >=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: biobb_common==4.2.0
+Requires-Dist: biobb_common==5.0.0
 
 [![](https://img.shields.io/github/v/tag/bioexcel/biobb_io?label=Version)](https://GitHub.com/bioexcel/biobb_io/tags/)
 [![](https://img.shields.io/pypi/v/biobb-io.svg?label=Pypi)](https://pypi.python.org/pypi/biobb-io/)
 [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
 [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -34,7 +33,7 @@ Requires-Dist: biobb_common==4.2.0
 
 [![](https://readthedocs.org/projects/biobb-io/badge/?version=latest&label=Docs)](https://biobb-io.readthedocs.io/en/latest/?badge=latest)
 [![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/)
-[![](https://img.shields.io/badge/Youtube-tutorial-blue?logo=youtube&logoColor=red)](https://www.youtube.com/watch?v=ou1DOGNs0xM)
+[![](https://img.shields.io/badge/Youtube-tutorials-blue?logo=youtube&logoColor=red)](https://www.youtube.com/@BioExcelCoE/search?query=biobb)
 [![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4)
 [![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas)
 
@@ -63,7 +62,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.0 2024.1
+v5.0.0 2024.2
 
 ### Installation
 Using PIP:
@@ -72,15 +71,15 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==4.2.0"
-        
+        pip install "biobb_io==5.0.0"
+
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
 Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==4.2.0"
+        conda install -c bioconda "biobb_io==5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html)
@@ -89,12 +88,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.0.0--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:5.0.0--pyhdfd78af_0 <command>
 
 
 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -106,7 +105,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.0--pyhdfd78af_0
 
 
 * Usage:

{biobb_io-4.2.0 → biobb_io-5.0.0}/README.md

@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_io?label=Conda)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_io?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_io)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_io?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_io:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_io)
 [![](https://img.shields.io/pypi/pyversions/biobb-io.svg?label=Python%20Versions)](https://pypi.org/project/biobb-io/)
@@ -12,7 +12,7 @@
 
 [![](https://readthedocs.org/projects/biobb-io/badge/?version=latest&label=Docs)](https://biobb-io.readthedocs.io/en/latest/?badge=latest)
 [![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/)
-[![](https://img.shields.io/badge/Youtube-tutorial-blue?logo=youtube&logoColor=red)](https://www.youtube.com/watch?v=ou1DOGNs0xM)
+[![](https://img.shields.io/badge/Youtube-tutorials-blue?logo=youtube&logoColor=red)](https://www.youtube.com/@BioExcelCoE/search?query=biobb)
 [![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4)
 [![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas)
 
@@ -41,7 +41,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-io.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.0 2024.1
+v5.0.0 2024.2
 
 ### Installation
 Using PIP:
@@ -50,15 +50,15 @@ Using PIP:
 
 * Installation:
 
-        pip install "biobb_io==4.2.0"
-        
+        pip install "biobb_io==5.0.0"
+
 * Usage: [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html)
 
 Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_io==4.2.0"
+        conda install -c bioconda "biobb_io==5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-io.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html)
@@ -67,12 +67,12 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_io:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_io:5.0.0--pyhdfd78af_0
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_io:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_io:5.0.0--pyhdfd78af_0 <command>
 
 
 The command list and specification can be found at the [Command Line documentation](https://biobb-io.readthedocs.io/en/latest/command_line.html).
@@ -84,7 +84,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_io.sif https://depot.galaxyproject.org/singularity/biobb_io:5.0.0--pyhdfd78af_0
 
 
 * Usage:

biobb_io-5.0.0/biobb_io/__init__.py

@@ -0,0 +1,5 @@
+from . import api
+
+name = "biobb_io"
+__all__ = ["api"]
+__version__ = "5.0.0"

biobb_io-5.0.0/biobb_io/api/__init__.py

@@ -0,0 +1,34 @@
+from . import (
+    alphafold,
+    api_binding_site,
+    canonical_fasta,
+    drugbank,
+    ideal_sdf,
+    ligand,
+    memprotmd_sim,
+    memprotmd_sim_list,
+    memprotmd_sim_search,
+    mmcif,
+    pdb,
+    pdb_cluster_zip,
+    pdb_variants,
+    structure_info,
+)
+
+name = "api"
+__all__ = [
+    "drugbank",
+    "ligand",
+    "pdb",
+    "alphafold",
+    "pdb_cluster_zip",
+    "pdb_variants",
+    "memprotmd_sim_list",
+    "memprotmd_sim_search",
+    "memprotmd_sim",
+    "api_binding_site",
+    "canonical_fasta",
+    "mmcif",
+    "ideal_sdf",
+    "structure_info",
+]

{biobb_io-4.2.0 → biobb_io-5.0.0}/biobb_io/api/alphafold.py

@@ -1,11 +1,21 @@
 #!/usr/bin/env python
 
 """Module containing the AlphaFold class and the command line interface."""
+
 import argparse
-from biobb_common.generic.biobb_object import BiobbObject
+from typing import Optional
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import check_output_path, check_mandatory_property, check_uniprot_code, download_af, write_pdb
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    check_uniprot_code,
+    download_af,
+    write_pdb,
+)
 
 
 class AlphaFold(BiobbObject):
@@ -20,6 +30,7 @@ class AlphaFold(BiobbObject):
             * **uniprot_code** (*str*) - (None) Uniprot code.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::
@@ -41,8 +52,7 @@ class AlphaFold(BiobbObject):
 
     """
 
-    def __init__(self, output_pdb_path,
-                 properties=None, **kwargs) -> None:
+    def __init__(self, output_pdb_path, properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -50,12 +60,10 @@ class AlphaFold(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = {
-            "out": {"output_pdb_path": output_pdb_path}
-        }
+        self.io_dict = {"out": {"output_pdb_path": output_pdb_path}}
 
         # Properties specific for BB
-        self.uniprot_code = properties.get('uniprot_code', None)
+        self.uniprot_code = properties.get("uniprot_code", None)
         self.properties = properties
 
         # Check the properties
@@ -63,8 +71,14 @@ class AlphaFold(BiobbObject):
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.output_pdb_path = check_output_path(self.io_dict["out"]["output_pdb_path"], "output_pdb_path", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.output_pdb_path = check_output_path(
+            self.io_dict["out"]["output_pdb_path"],
+            "output_pdb_path",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -77,14 +91,18 @@ class AlphaFold(BiobbObject):
         if self.check_restart():
             return 0
 
-        check_mandatory_property(self.uniprot_code, 'uniprot_code', self.out_log, self.__class__.__name__)
+        check_mandatory_property(
+            self.uniprot_code, "uniprot_code", self.out_log, self.__class__.__name__
+        )
 
         self.uniprot_code = self.uniprot_code.strip().upper()
 
         check_uniprot_code(self.uniprot_code, self.out_log, self.__class__.__name__)
 
         # Downloading PDB file
-        pdb_string = download_af(self.uniprot_code, self.out_log, self.global_log, self.__class__.__name__)
+        pdb_string = download_af(
+            self.uniprot_code, self.out_log, self.global_log, self.__class__.__name__
+        )
         write_pdb(pdb_string, self.output_pdb_path, None, self.out_log, self.global_log)
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -92,31 +110,44 @@ class AlphaFold(BiobbObject):
         return 0
 
 
-def alphafold(output_pdb_path: str, properties: dict = None, **kwargs) -> int:
+def alphafold(output_pdb_path: str, properties: Optional[dict] = None, **kwargs) -> int:
     """Execute the :class:`AlphaFold <api.alphafold.AlphaFold>` class and
     execute the :meth:`launch() <api.alphafold.AlphaFold.launch>` method."""
 
-    return AlphaFold(output_pdb_path=output_pdb_path,
-                     properties=properties, **kwargs).launch()
+    return AlphaFold(
+        output_pdb_path=output_pdb_path, properties=properties, **kwargs
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="This class is a wrapper for downloading a PDB structure from the Protein Data Bank.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="This class is a wrapper for downloading a PDB structure from the Protein Data Bank.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('-o', '--output_pdb_path', required=True, help="Path to the output PDB file. Accepted formats: pdb.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_pdb_path",
+        required=True,
+        help="Path to the output PDB file. Accepted formats: pdb.",
+    )
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    alphafold(output_pdb_path=args.output_pdb_path,
-              properties=properties)
+    alphafold(output_pdb_path=args.output_pdb_path, properties=properties)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

{biobb_io-4.2.0 → biobb_io-5.0.0}/biobb_io/api/api_binding_site.py

@@ -1,13 +1,22 @@
 #!/usr/bin/env python
 
 """Module containing the ApiBindingSite class and the command line interface."""
+
 import argparse
 import json
-from biobb_common.generic.biobb_object import BiobbObject
+from typing import Optional
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import check_output_path, check_mandatory_property, download_binding_site, write_json
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    download_binding_site,
+    write_json,
+)
 
 
 class ApiBindingSite(BiobbObject):
@@ -22,6 +31,7 @@ class ApiBindingSite(BiobbObject):
             * **pdb_code** (*str*) - (None) RSCB PDB code.
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::
@@ -43,8 +53,7 @@ class ApiBindingSite(BiobbObject):
 
     """
 
-    def __init__(self, output_json_path,
-                 properties=None, **kwargs) -> None:
+    def __init__(self, output_json_path, properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -52,12 +61,10 @@ class ApiBindingSite(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = {
-            "out": {"output_json_path": output_json_path}
-        }
+        self.io_dict = {"out": {"output_json_path": output_json_path}}
 
         # Properties specific for BB
-        self.pdb_code = properties.get('pdb_code', None)
+        self.pdb_code = properties.get("pdb_code", None)
         self.properties = properties
 
         # Check the properties
@@ -65,8 +72,14 @@ class ApiBindingSite(BiobbObject):
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.output_json_path = check_output_path(self.io_dict["out"]["output_json_path"], "output_json_path", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.output_json_path = check_output_path(
+            self.io_dict["out"]["output_json_path"],
+            "output_json_path",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -80,16 +93,24 @@ class ApiBindingSite(BiobbObject):
             return 0
         # self.stage_files()
 
-        check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
+        check_mandatory_property(
+            self.pdb_code, "pdb_code", self.out_log, self.__class__.__name__
+        )
 
         self.pdb_code = self.pdb_code.strip().lower()
         url = "https://www.ebi.ac.uk/pdbe/api/pdb/entry/binding_sites/%s"
 
         # get JSON object
-        json_string = download_binding_site(self.pdb_code, url, self.out_log, self.global_log)
+        json_string = download_binding_site(
+            self.pdb_code, url, self.out_log, self.global_log
+        )
 
         # get number of binding sites
-        fu.log('%d binding sites found' % (len(json.loads(json_string)[self.pdb_code])), self.out_log, self.global_log)
+        fu.log(
+            "%d binding sites found" % (len(json.loads(json_string)[self.pdb_code])),
+            self.out_log,
+            self.global_log,
+        )
 
         # write JSON file
         write_json(json_string, self.output_json_path, self.out_log, self.global_log)
@@ -99,31 +120,46 @@ class ApiBindingSite(BiobbObject):
         return 0
 
 
-def api_binding_site(output_json_path: str, properties: dict = None, **kwargs) -> int:
+def api_binding_site(
+    output_json_path: str, properties: Optional[dict] = None, **kwargs
+) -> int:
     """Execute the :class:`ApiBindingSite <api.api_binding_site.ApiBindingSite>` class and
     execute the :meth:`launch() <api.api_binding_site.ApiBindingSite.launch>` method."""
 
-    return ApiBindingSite(output_json_path=output_json_path,
-                          properties=properties, **kwargs).launch()
+    return ApiBindingSite(
+        output_json_path=output_json_path, properties=properties, **kwargs
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="This class is a wrapper for the PDBe REST API Binding Sites endpoint", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="This class is a wrapper for the PDBe REST API Binding Sites endpoint",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('-o', '--output_json_path', required=True, help="Path to the JSON file with the binding sites for the requested structure. Accepted formats: json.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_json_path",
+        required=True,
+        help="Path to the JSON file with the binding sites for the requested structure. Accepted formats: json.",
+    )
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    api_binding_site(output_json_path=args.output_json_path,
-                     properties=properties)
+    api_binding_site(output_json_path=args.output_json_path, properties=properties)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()

{biobb_io-4.2.0 → biobb_io-5.0.0}/biobb_io/api/canonical_fasta.py

@@ -1,11 +1,20 @@
 #!/usr/bin/env python
 
 """Module containing the CanonicalFasta class and the command line interface."""
+
 import argparse
-from biobb_common.generic.biobb_object import BiobbObject
+from typing import Optional
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools.file_utils import launchlogger
-from biobb_io.api.common import check_output_path, check_mandatory_property, download_fasta, write_fasta
+
+from biobb_io.api.common import (
+    check_mandatory_property,
+    check_output_path,
+    download_fasta,
+    write_fasta,
+)
 
 
 class CanonicalFasta(BiobbObject):
@@ -21,6 +30,7 @@ class CanonicalFasta(BiobbObject):
             * **api_id** (*str*) - ("pdbe") Identifier of the PDB REST API from which the PDB structure will be downloaded. Values: pdbe (`PDB in Europe REST API <https://www.ebi.ac.uk/pdbe/pdbe-rest-api>`_), pdb (`RCSB PDB REST API <https://data.rcsb.org/>`_), mmb (`MMB PDB mirror API <http://mmb.irbbarcelona.org/api/>`_).
             * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
             * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
+            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
 
     Examples:
         This is a use example of how to use the building block from Python::
@@ -43,8 +53,7 @@ class CanonicalFasta(BiobbObject):
 
     """
 
-    def __init__(self, output_fasta_path,
-                 properties=None, **kwargs) -> None:
+    def __init__(self, output_fasta_path, properties=None, **kwargs) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -52,13 +61,11 @@ class CanonicalFasta(BiobbObject):
         self.locals_var_dict = locals().copy()
 
         # Input/Output files
-        self.io_dict = {
-            "out": {"output_fasta_path": output_fasta_path}
-        }
+        self.io_dict = {"out": {"output_fasta_path": output_fasta_path}}
 
         # Properties specific for BB
-        self.pdb_code = properties.get('pdb_code', None)
-        self.api_id = properties.get('api_id', 'pdbe')
+        self.pdb_code = properties.get("pdb_code", None)
+        self.api_id = properties.get("api_id", "pdbe")
         self.properties = properties
 
         # Check the properties
@@ -66,8 +73,14 @@ class CanonicalFasta(BiobbObject):
         self.check_arguments()
 
     def check_data_params(self, out_log, err_log):
-        """ Checks all the input/output paths and parameters """
-        self.output_fasta_path = check_output_path(self.io_dict["out"]["output_fasta_path"], "output_fasta_path", False, out_log, self.__class__.__name__)
+        """Checks all the input/output paths and parameters"""
+        self.output_fasta_path = check_output_path(
+            self.io_dict["out"]["output_fasta_path"],
+            "output_fasta_path",
+            False,
+            out_log,
+            self.__class__.__name__,
+        )
 
     @launchlogger
     def launch(self) -> int:
@@ -80,12 +93,16 @@ class CanonicalFasta(BiobbObject):
         if self.check_restart():
             return 0
 
-        check_mandatory_property(self.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__)
+        check_mandatory_property(
+            self.pdb_code, "pdb_code", self.out_log, self.__class__.__name__
+        )
 
         self.pdb_code = self.pdb_code.strip().lower()
 
         # Downloading PDB file
-        pdb_string = download_fasta(self.pdb_code, self.api_id, self.out_log, self.global_log)
+        pdb_string = download_fasta(
+            self.pdb_code, self.api_id, self.out_log, self.global_log
+        )
         write_fasta(pdb_string, self.output_fasta_path, self.out_log, self.global_log)
 
         self.check_arguments(output_files_created=True, raise_exception=False)
@@ -93,31 +110,46 @@ class CanonicalFasta(BiobbObject):
         return 0
 
 
-def canonical_fasta(output_fasta_path: str, properties: dict = None, **kwargs) -> int:
+def canonical_fasta(
+    output_fasta_path: str, properties: Optional[dict] = None, **kwargs
+) -> int:
     """Execute the :class:`CanonicalFasta <api.canonical_fasta.CanonicalFasta>` class and
     execute the :meth:`launch() <api.canonical_fasta.CanonicalFasta.launch>` method."""
 
-    return CanonicalFasta(output_fasta_path=output_fasta_path,
-                          properties=properties, **kwargs).launch()
+    return CanonicalFasta(
+        output_fasta_path=output_fasta_path, properties=properties, **kwargs
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="This class is a wrapper for downloading a FASTA structure from the Protein Data Bank.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('-o', '--output_fasta_path', required=True, help="Path to the canonical FASTA file. Accepted formats: fasta.")
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument(
+        "-o",
+        "--output_fasta_path",
+        required=True,
+        help="Path to the canonical FASTA file. Accepted formats: fasta.",
+    )
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    canonical_fasta(output_fasta_path=args.output_fasta_path,
-                    properties=properties)
+    canonical_fasta(output_fasta_path=args.output_fasta_path, properties=properties)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()